Actualiser .gitmodules

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "sumalibs"]
 	path = sumalibs
-	url = https://git.metabarcoding.org/obitools/sumalibs.git
+	url = https://forge.metabarcoding.org/obitools/sumalibs.git

Makefile

@@ -1,16 +1,17 @@
-EXEC=sumaclust
+PREFIX=/usr/local
 
-SUMACLUST_SRC= sumaclust.c \
-               mtcompare_sumaclust.c
+CFLAGS=-I$(PREFIX)/include
 
-             
-SUMACLUST_OBJ= $(patsubst %.c,%.o,$(SUMACLUST_SRC))
+EXEC = sumaclust
 
+SUMACLUST_SRC = sumaclust.c \
+                mtcompare_sumaclust.c
 
-SRCS= $(SUMACLUST_SRC)
+SUMACLUST_OBJ = $(patsubst %.c,%.o,$(SUMACLUST_SRC))
 
-LIB= -lfasta -llcs -lfile -lutils -lm #-ll
+SRCS = $(SUMACLUST_SRC)
 
+LIB = -lsuma -lm #-ll
 
 include ./global.mk
 
@@ -31,8 +32,8 @@ else
         LFLAGS = 
 endif
 
-sumaclust: $(SUMACLUST_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS)
-	$(CC) $(LDFLAGS) -o $@ $(LFLAGS) $(SUMACLUST_OBJ) $(LIB) $(LIBFASTAPATH) $(LIBLCSPATH) $(LIBFILEPATH) $(LIBUTILSPATH)
+sumaclust: $(SUMACLUST_OBJ) $(LIBSUMA)
+	$(CC) $(LDFLAGS) -o $@ $(LFLAGS) $(SUMACLUST_OBJ) $(LIB) $(LIBSUMAPATH)
 	
 ########
 #
@@ -41,12 +42,11 @@ sumaclust: $(SUMACLUST_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS)
 ########
 
 clean:
-	rm -f *.o	
-	rm -f *.P
+	rm -f $(SUMACLUST_OBJ)	
 	rm -f $(EXEC)
-	$(MAKE) -C ./sumalibs/libfasta clean
-	$(MAKE) -C ./sumalibs/liblcs clean
-	$(MAKE) -C ./sumalibs/libfile clean
-	$(MAKE) -C ./sumalibs/libutils clean
+	$(MAKE) -C ./sumalibs clean
+
+install: all
+	install -d $(DESTDIR)$(PREFIX)/bin/
+	install -m 755 $(EXEC) $(DESTDIR)$(PREFIX)/bin/
 
-		

README.md

@@ -0,0 +1 @@
+[See the wiki](https://git.metabarcoding.org/obitools/sumaclust/wikis/home)

global.mk

@@ -1,13 +1,7 @@
 
-LIBFASTAPATH = -L./sumalibs/libfasta
-LIBLCSPATH   = -L./sumalibs/liblcs
-LIBFILEPATH  = -L./sumalibs/libfile
-LIBUTILSPATH = -L./sumalibs/libutils
+LIBSUMAPATH = -L./sumalibs
 
-LIBFASTA = ./sumalibs/libfasta/libfasta.a
-LIBLCS   = ./sumalibs/liblcs/liblcs.a
-LIBFILE  = ./sumalibs/libfile/libfile.a
-LIBUTILS = ./sumalibs/libutils/libutils.a
+LIBSUMA = ./sumalibs/libsuma.a
 
 CC=gcc
 LDFLAGS=
@@ -32,14 +26,5 @@ default: all
 #
 ########
 
-./sumalibs/libfasta/libfasta.a:
-	$(MAKE) -C ./sumalibs/libfasta
-
-./sumalibs/liblcs/liblcs.a:
-	$(MAKE) -C ./sumalibs/liblcs
-
-./sumalibs/libfile/libfile.a:
-	$(MAKE) -C ./sumalibs/libfile
-
-./sumalibs/libutils/libutils.a:
-	$(MAKE) -C ./sumalibs/libutils
+./sumalibs/libsuma.a:
+	$(MAKE) -C ./sumalibs

mtcompare_sumaclust.c

@@ -15,10 +15,10 @@
 #include <math.h>
 #include <sys/time.h>
 
-#include "./sumalibs/libfasta/sequence.h"
-#include "./sumalibs/libutils/utilities.h"
-#include "./sumalibs/liblcs/upperband.h"
-#include "./sumalibs/liblcs/sse_banded_LCS_alignment.h"
+#include "sumalibs/libfasta/sequence.h"
+#include "sumalibs/libutils/utilities.h"
+#include "sumalibs/liblcs/upperband.h"
+#include "sumalibs/liblcs/sse_banded_LCS_alignment.h"
 
 #include "sumaclust.h"
 

sumaclust.c

@@ -12,18 +12,18 @@
 #include <math.h>
 #include <sys/time.h>
 
-#include "./sumalibs/libutils/utilities.h"
-#include "./sumalibs/libfasta/sequence.h"
-#include "./sumalibs/libfasta/fasta_header_parser.h"
-#include "./sumalibs/libfasta/fasta_header_handler.h"
-#include "./sumalibs/libfasta/fasta_seq_writer.h"
-#include "./sumalibs/liblcs/upperband.h"
-#include "./sumalibs/liblcs/sse_banded_LCS_alignment.h"
+#include "sumalibs/libutils/utilities.h"
+#include "sumalibs/libfasta/sequence.h"
+#include "sumalibs/libfasta/fasta_header_parser.h"
+#include "sumalibs/libfasta/fasta_header_handler.h"
+#include "sumalibs/libfasta/fasta_seq_writer.h"
+#include "sumalibs/liblcs/upperband.h"
+#include "sumalibs/liblcs/sse_banded_LCS_alignment.h"
 
 #include "mtcompare_sumaclust.h"
 #include "sumaclust.h"
 
-#define VERSION "1.0.10"
+#define VERSION "1.0.36"
 
 
 /* ----------------------------------------------- */
@@ -73,9 +73,10 @@ static void PrintHelp()
         PP      " -f       : Output in FASTA format is deactivated.\n");
         PP      "\n");
         PP      "------------------------------------------------------------\n");
-        PP      " Argument : the nucleotide dataset to cluster\n");
+        PP      " Argument : the nucleotide dataset to cluster (or nothing   \n");
+        PP      "            if the standard input should be used).          \n");
         PP      "------------------------------------------------------------\n");
-        PP		" http://metabarcoding.org/sumatra\n");
+        PP		" http://metabarcoding.org/sumaclust\n");
         PP      "------------------------------------------------------------\n\n");
 }
 
@@ -584,7 +585,7 @@ void putSeqInCluster(fastaSeqPtr* seq, fastaSeqPtr* center, double score)
 }
 
 
-int compare(fastaSeqPtr* db,  int n, BOOL fastOption, double threshold, BOOL normalize, int reference, BOOL lcsmode,
+int compare(fastaSeqPtr* db, int n, BOOL fastOption, double threshold, BOOL normalize, int reference, BOOL lcsmode,
 		double max_ratio)
 {
 	double       score;
@@ -722,7 +723,7 @@ int compare(fastaSeqPtr* db,  int n, BOOL fastOption, double threshold, BOOL nor
 	free(iseq1-sizeForSeqs+lmax);
 	free(iseq2-sizeForSeqs+lmax);
 
-	if (normalize && reference == ALILEN)
+	if (normalize && (reference == ALILEN))
 		free(address);
 
 	return(k);
@@ -794,7 +795,6 @@ int main(int argc, char** argv)
 	BOOL			reverse		     = FALSE;
 	BOOL			onlyATGC	     = TRUE;
 	int             reference        = ALILEN;
-	int             ndb              = 0;
 	int				nproc            = 1;
 	BOOL			printBIOM        = FALSE;
 	BOOL			printOTUtable    = FALSE;
@@ -941,10 +941,6 @@ int main(int argc, char** argv)
 		}
 	}
 
-	ndb = argc - optind;
-	if (ndb != 1)
-        errflag++;
-
 	if (errflag)
 		ExitUsage(errflag);
 
@@ -965,6 +961,7 @@ int main(int argc, char** argv)
 
 	fprintf(stderr,"Reading dataset...");
 	db = seq_readAllSeq2(argv[optind], TRUE, onlyATGC);
+
 	fprintf(stderr,"\n%d sequences\n",db.count);
 
 	if (db.count == 0)
@@ -1040,7 +1037,6 @@ int main(int argc, char** argv)
 	// FASTA file
 	if (printFASTA)
 	{
-
 		if (printFASTAtofile)
 		{
 			FASTA_output = fopen(FASTA_file_name, "w");

sumaclust_user_manual.md

@@ -29,7 +29,8 @@ Untar the archive, go into the newly created directory and compile:
 ```
 tar –zxvf sumaclust_v[x.x.xx].tar.gz
 cd sumaclust_v[x.x.xx]
-make
+make -C sumalibs install
+make install
 ```
 
 You can compile Sumaclust with `clang`, which deactivates `OpenMP`, with:
@@ -46,12 +47,12 @@ Sumaclust clusters sequences using the same clustering algorithm as UCLUST and C
 
 #### Input
 
-Input file must be in FASTA format.
+The input can be either the standard input (stdin), or a file in FASTA format.
 
 #### Usage
 
 ```
-sumaclust [-l|L|a|n|r|d|e|o|g|f] [-t threshold_value] [-s sorting_key] [-R maximum_ratio] [-p number_of_threads] [-B file_name_for_BIOM-formatted_output] [-O file_name_for_OTU_table-formatted_output] [-F file_name_for_FASTA-formatted_output] dataset
+sumaclust [-l|L|a|n|r|d|e|o|g|f] [-t threshold_value] [-s sorting_key] [-R maximum_ratio] [-p number_of_threads] [-B file_name_for_BIOM-formatted_output] [-O file_name_for_OTU_table-formatted_output] [-F file_name_for_FASTA-formatted_output] [dataset]
 ```
 
 Argument: the sequence dataset to cluster.